Research workbench
Human PDE10A, 6-chloro-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl- 2H-[1,2,4]TRIAZOL-3-yl)-ethyl]-[1,2,4]TRIAZOLO[1,5-A]PYRIDINE, 2.20A, H3, RFREE=23.5%
Analyse Human PDE10A, 6-chloro-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EDI
- Type
- protein
- Length
- 1,263 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A
- EC
- 3.1.4.17, 3.1.4.35
- UniProt
- Q9Y233
- Ligands
- 5M9, ZN, MG
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 313 | 71% helix, 0% strand | Q9Y233 |
| B | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 320 | 70% helix, 0% strand | Q9Y233 |
| D | Camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17, 3.1.4.35) | protein | 317 | 72% helix, 0% strand | Q9Y233 |
Ligands and binding sites
- 5M9 · 6-chloranyl-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-a]pyridine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.74 | 0.78 | 86 | empty |
| 2 | 400 | 0.73 | 0.83 | 52 | MG, 5M9 |
| 3 | 423 | 0.73 | 0.83 | 51 | MG, 5M9 |
| 4 | 448 | 0.73 | 0.82 | 50 | MG, 5M9 |
| 5 | 406 | 0.72 | 0.83 | 53 | MG, 5M9 |
Interfaces
5 interfaces between chains.
- A–C · 721 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 713 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 707 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 527 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 53 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, artifact).
Compared structures
- 5EDI · CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y233
- Elsewhere: RCSB PDB 5EDI · PDBe 5EDI · UniProt Q9Y233
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